Re: [DIYbio] Electronic requirements for redesign of Arduino PCR thermal cycler

Oh, nice idea! I wonder if even plastic capillaries at that scale are conductive enough to work, I could see it being possible to make "pinch-off" capillaries that you fill (by capillary action? :)) and pinch, then lay on your micro-cycler made with a peltier, two heatsinks, an LM35 temp sensor, and an Arduino micro or similar.

As usual with Peltiers, the big ask is current, so the complexity arises from ensuring enough is delivered from a suitable power source through the peltiers.

I wonder if a "constant heat flow" design couldn't be knocked together with a heating element atop the fins on the reaction side, so heat is conducted downwards through the fins to the tubes, and cooling is achieved by ceasing to apply heat and letting the heatsink distribute what remains. But, that's only marginally simpler than fixing up a cooling fan to a simple heat-block anyway and just doing coil-heating-air-cooling, which is possibly as efficient as these things get until you start coming full-circle to convective PCR (pun welcomed but not intended)..

On 27/02/15 08:35, Mac Cowell wrote:

Also, just want to point out that if you fill capillary glass tranfer
pipettes (typically like $20 for 100, with volumes selectable from
0.5-50uL), they fit perfectly in the valleys of many
sawtooth-style sinks (cheap). The surface to volume ratio is such that I
don't think a heated lid is necessary.  Imaging from above is possible,
potentially enabling qpcr-like applications.

They are just a bit of a pain to work with.

But the thermocycler is so simple in this case. Peltier, sawtooth heat
sink with 5-10 ridges, mosfet for switching power, embedded
thermocouple, microcontroller, and 5-10 glass capillaries, one per sample.

Cheers
Mac

On Friday, February 27, 2015, Mac Cowell <mac@diybio.org

<mailto:mac@diybio.org>> wrote:

    The reaction mixture will condense on the coldest part of the pcr
    tube, for instance, any surface not enclosed in the main heated
    block and exposed to ambient air.

    One solution is to establish a temperature gradient from the top of
    the cap to the block by touching the cap with a second hot surface,
    preferably hotter than the main block such radiative and conductive
    heat transfer from the heated lid raises the temperature of all
    surfaces of the pcr tube exposed to air above the current
    temperature of the block.

    But you don't need s Peltier to do this. You just need a heat source
    you can keep at a constant temperature guaranteed to be hotter than
    any of the pcr temps.

    It would be interesting to explore a hybrid design combining
    dynamic conductive heating in the tube block with constant radiative
    heating from a lamp or hot air flow positioned at just the right
    distance, instead of a heated lid in constant contact with the cap.
    Can the radiative heat source be set up to always add +20C to the
    exposed cap and 5-10 C to the reaction mixture? If so, perhaps such
    a design could lead to faster ramp times, by switching the radiator
    off during cooling.

    Does the transparent plastic most pcr tubes are made from absorb IR?

    Or maybe all that matters is if the reaction mixture absorbs the
    radiative energy. Not sure. Would pcr work in a transparent Quartz
    vessel in a freezer that was pulsed by a powerful IR source? Or
    would that be condensation city?

    Cheers
    Mac

    On Thursday, February 26, 2015, Andy Morgan
    <andrew.r.morgan@gmail.com

    <javascript:_e(%7B%7D,'cvml','andrew.r.morgan@gmail.com');>> wrote:

        Thanks for the heads up Josiah.

        That's a bit annoying, I was hoping that I could have the lid at
        the same temperature as the tubes, allowing me to run the whole
        thing off of just the one simple circuit described in the
        original instructable.

        Perhaps I'll look into using one peltier element for the base
        and another smaller one for the lid, although that might mean
        I'd have to hook up a whole other arduino board and solid state
        relay. Not to mention that all sounding a wee bit over my head.
        If I could hook them both up to the one arduino board that might
        be a little bit simpler though.

        I came across this design
        (http://2013.igem.org/Team:Paris_Saclay/PS-PCR/detailed_description)
        that was build (and apparently for only 30 euros!) using peltier
        elements, but the electronic schematics look intense.

        On Friday, February 27, 2015 at 2:12:14 PM UTC+13, Josiah Zayner
        wrote:

            Keeping the lid at a constant temp of ~90C will generally
            suffice. Most PCR machines hold the lid at 90C - 105C.

            I have tried doing the lid at same temperature as the tubes
            but received condensation. I think this might have been
            because of the different heat transfer rates? Maybe you can
            figure it out?

            Looking on eBay these days you can buy most of the parts for
            the Arduino thermalcycler for much cheaper than the $85USD
            pricetag (inexpensive Arduino boards &c). Also, keep on eye
            out on eBay for thermal cyclers. Sometimes people don't know
            what the actual equipment is so they just list it as brand
            and product names so searching directly for brand names
            help. I have found some for under $100 that work great
            though this is from the US, so who knows what you might find?



            Josiah




            On Thursday, February 26, 2015 at 3:02:09 PM UTC-8, Andy
            Morgan wrote:

                Ah it all becomes clear, I was wondering why they listed
                a 12V power supply AND a regular power cable.

                Thanks Simon.

                On Friday, February 27, 2015 at 8:22:16 AM UTC+13, Simon
                Field wrote:

                    I presume the power supply is simply for the Arduino
                    part of the project, which is unchanged from the
                    original. In fact, the only thing that has changed
                    is the heater. It's like swapping a 40 watt light
                    bulb for a 100 watt light bulb. You don't have to
                    change anything else.

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